Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE 19716, USA.
Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
G3 (Bethesda). 2023 Aug 9;13(8). doi: 10.1093/g3journal/jkad097.
The clapper rail (Rallus crepitans), of the family Rallidae, is a secretive marsh bird species that is adapted for high salinity habitats. They are very similar in appearance to the closely related king rail (R. elegans), but while king rails are limited primarily to freshwater marshes, clapper rails are highly adapted to tolerate salt marshes. Both species can be found in brackish marshes where they freely hybridize, but the distribution of their respective habitats precludes the formation of a continuous hybrid zone and secondary contact can occur repeatedly. This system, thus, provides unique opportunities to investigate the underlying mechanisms driving their differential salinity tolerance as well as the maintenance of the species boundary between the 2 species. To facilitate these studies, we assembled a de novo reference genome assembly for a female clapper rail. Chicago and HiC libraries were prepared as input for the Dovetail HiRise pipeline to scaffold the genome. The pipeline, however, did not recover the Z chromosome so a custom script was used to assemble the Z chromosome. We generated a near chromosome level assembly with a total length of 994.8 Mb comprising 13,226 scaffolds. The assembly had a scaffold N50 was 82.7 Mb, L50 of four, and had a BUSCO completeness score of 92%. This assembly is among the most contiguous genomes among the species in the family Rallidae. It will serve as an important tool in future studies on avian salinity tolerance, interspecific hybridization, and speciation.
鼓翼杓鹬（Rallus crepitans），属于杓鹬科，是一种适应高盐度栖息地的隐匿性沼泽鸟类。它们的外观与亲缘关系密切的王杓鹬（R. elegans）非常相似，但王杓鹬主要局限于淡水沼泽，而鼓翼杓鹬则高度适应盐沼环境。这两个物种都可以在半咸水沼泽中找到，它们在那里自由杂交，但由于它们各自栖息地的分布，形成了一个连续的杂交区，而且可以反复发生二次接触。因此，这个系统为研究导致它们不同盐度耐受性的潜在机制以及维持这两个物种之间的物种边界提供了独特的机会。为了促进这些研究，我们为一只雌性鼓翼杓鹬组装了一个从头开始的参考基因组组装。为了组装基因组，我们用芝加哥和 HiC 文库作为输入来制备 Dovetail HiRise 管道的文库。然而，该管道未能恢复 Z 染色体，因此我们使用了一个定制脚本来组装 Z 染色体。我们生成了一个接近染色体水平的组装，总长度为 994.8 Mb，包含 13226 个支架。组装的支架 N50 为 82.7 Mb，L50 为 4，具有 92%的 BUSCO 完整性评分。这个组装是在杓鹬科的物种中最连续的基因组之一。它将成为未来研究鸟类盐度耐受性、种间杂交和物种形成的重要工具。
